Changes

= Variants that Alter Protein Function =

= Variants that Alter Protein Function =

In the genome of an average individual (as represented by the exome sequenced individuals contributed for chip design), we expect to see XXX nonsynonymous variants, XXX splice variants and XXX stop altering variants.

In the genome of an average individual (as represented by the exome sequenced individuals contributed for chip design), we expect to see ~8,000 - 10,000 nonsynonymous variants, ~200 - 300 splice variants and ~80 - 100 stop altering variants.

== Non-synonymous Variants ==

== Non-synonymous Variants ==

We tallied 1,081,805 nonsynonymous and 613,106 variants seen at least once across ~12,000 sequenced samples. Among the non-synonymous variants, the majority were seen only once (634,787) or twice (157,261), as expected. Of the remaining variants (289,757), a total of 254,035 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was XXX for variants in dbSNP 132 and XXX for non dbSNP variants.

We tallied 1,107,05 nonsynonymous variants seen at least once across ~12,000 sequenced samples. Among the non-synonymous variants, the majority were seen only once (646,888) or twice (163,044), as expected. Of the remaining variants (297,119), a total of 260,054 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was 2.0 in the full set of variants and 2.49 in the set of variants that were seen at least three times and in two or more studies.

These variants include %%% of the XXX nonsynonymous variants detected in average genome through exome sequencing.

The set of variants selected for array design is estimated to include 97-98% of the nonsynonymous variants detected in average genome through exome sequencing.

 

In the Illumina platform, 232,125 of these variants were assigned an assay design score >0.50 using a probe that didn't overlap nearby SNPs seen at least 100 times. These are considered candidates for manufacturing. These variants include %%% of the XXX nonsynonymous variants detected in an average genome through exome sequencing. The actual number that can be detected by genotyping arrays will depend on the fraction of successfully manufactured probes, expected to be 85-90%.

== Splice Variants ==

== Splice Variants ==